Variant report

Variant	rs2254546
Chromosome Location	chr8:11343680-11343681
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:118857357..118859002-chr8:11343082..11345568,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs13256690	0.92[ASN][1000 genomes]
rs13277113	0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1382568	0.86[ASN][1000 genomes]
rs1478895	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1478900	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1478901	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1531577	0.92[ASN][1000 genomes]
rs1564267	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17153385	0.85[MEX][hapmap]
rs2061831	0.84[ASN][1000 genomes]
rs2244234	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2250412	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2250788	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2251056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254660	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2254891	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2409780	0.82[ASN][1000 genomes]
rs2618444	0.82[ASN][1000 genomes]
rs2618455	0.82[CHB][hapmap];0.85[MEX][hapmap]
rs2618456	0.82[CHB][hapmap]
rs2618457	0.81[CHB][hapmap]
rs2618473	0.86[ASN][1000 genomes]
rs2618476	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2618478	0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2618479	0.83[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2618480	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2618481	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2736332	0.84[ASN][1000 genomes]
rs2736335	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2736340	0.86[ASN][1000 genomes]
rs2736343	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2736344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2736345	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2736353	0.81[CHB][hapmap]
rs2736354	0.81[CHB][hapmap];0.85[MEX][hapmap]
rs2736355	0.81[CHB][hapmap]
rs35393613	0.89[ASN][1000 genomes]
rs4840565	0.96[ASN][1000 genomes]
rs4840568	0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs62489069	0.89[ASN][1000 genomes]
rs6993775	0.81[CHB][hapmap]
rs7812879	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs922483	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9693589	0.82[ASN][1000 genomes]
rs9694294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs998682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs998683	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1022074	chr8:11292256-11394526	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2762725	chr8:11322997-11350721	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Systemic lupus erythematosus	23273568	GWAS catalog
Kawasaki disease	22446962	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2254546	FLJ10661	cis	cerebellum	SCAN
rs2254546	BLK	cis	multi-tissue	Pritchard
rs2254546	C8orf13	cis	multi-tissue	Pritchard
rs2254546	FAM167A	cis	lymphoblastoid	seeQTL
rs2254546	C8orf79	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11338200-11350000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr8:11338800-11343800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:11339000-11353800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:11341600-11343800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr8:11342200-11348600	ZNF genes & repeats	GM12878-XiMat	blood
6	chr8:11343200-11344400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
7	chr8:11343400-11344000	Enhancers	Primary B cells from cord blood	blood

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